The baptismal font made of marble and alabaster has been built by Franz Döteber in 1614-15. On it are portrayed biblical scenes. It was restored in 2009.
The architectural design of the Neo-Gothic "Jesus" Altar was completed in 1888 by Constantin Lipsius (1832-1894). The altar stood in the church until the interior renovation of 1964 and was brought back in 2016 after the St. Paul Altar was returned to the new University Church of St. Paul in 2014. The relief in the middle of the altar presents the Last Supper of Jesus with his disciples. It was crafted by Oskar Rassau (1843/1912). The other reliefs show scenes from the life of Jesus.

In the sanctuary are the portraits of the Superintendents of Leipzig since the introduction or the Reformation. The oldest of these portraits date back to 1614.

Under the bronze epitaph lie the remains of Johann Sebastian Bach since 1950. The remains were found in1894 on the St. John's Church cemetery.  These were retained inside the St. John's Church since 1900. When the church was destroyed in World War II, the remains were translated to the St. Thomas Church.

Noteworthly are the numerous epitaphs (memorial plates) throughout the church. The oldest one is for Knight Harras (+1451). This can be found under the south balcony to the left of the side entrance. In the northcrossing hangs the epitaph of Councilman Daniel Leicher (1612).

Originally the windows of the St. Thomas Church were made of a simple ornament glass. The colorful windows in the sanctuary and on the south side of the church were installed after 1889. In the sanctuary, the windows portray the followong scenes: the birth, the baptism, the resurrection of Jesus and the disciples of Emmaus. In May 2000, the only window destroyed during World War II was replaced with the Thomas Window designed by Hans-Gottfried von Stockhausen.

On the south side, the windows represent (from left to right) the following scenes: Memorial window for the fallen soldiers of World War I,  King Gustav II. Adolf of Sweden, Johann Sebastian Bach, Martin Luther with Elector Friedrich the Wise of Saxony (left) and Philipp Melanchthon (right); Felix Mendelssohn Bartholdy (seit 1997) and Kaiser Wilhelm I.

In October 2009 the serial has been added by the peace window designed by David Schnell.